After the first season of The Monkees, Mike Nesmith complained to the press that "we're being passed off as something we're not", in that they didn't play instruments on their records. And he challenged the control of Don Kirschner.

I'm watching the second season now. I've seen a couple of episodes with no Mike (except for pre-taped musical numbers). I've seen an episode where a character is looking at all four of them and calls Mike (only) a "troublemaker". Then there's an episode where Davy, Micky, and Peter are hired to work on what turns out to be a pirate ship. Cut to onboard, Mike is with them, but right away gets seasick and is sent below to lie down. He is not seen for the rest of the episode.

What's the story? Were they getting him back for speaking out?

Mike had his tonsils out during production of season 2, so he missed a couple of episodes. The Pirate Ship episode- Mike legitemately got seasick, and missed the rest of the episode because he was seasick (really).
Rafelson and Schneider did not have any more trouble with Mike than the other three from what I've read over the years.